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Series GSE274196 Query DataSets for GSE274196
Status Public on Aug 24, 2024
Title RNA quality control by CCR4 safeguards chromatin integrity and centromere function in Arabidopsis [EM-seq]
Organism Arabidopsis thaliana
Experiment type Methylation profiling by high throughput sequencing
Summary The centromere is a pivotal chromatin domain that ensures accurate chromosome segregation during cell division. However, the epigenome regulation of the centromere and its impact on centromere function remain largely elusive. Here in the model plant Arabidopsis, we show that CCR4, the catalytic subunit of the RNA deadenylation complex CCR4-NOT, is essential for maintenance of the centromere epigenome and chromosome integrity. We demonstrate that CCR4 is involved in shortening of the poly(A) tails of transcripts originated from centromeric transposons and repeats, thereby promoting the production of small interfering RNAs (siRNAs). The CCR4-dependent siRNAs guide non-CG DNA methylation at centromere repeats, and CCR4 cooperates with canonical DNA methylation pathways to enhance centromeric H3K9 methylation and ensure mitotic chromosome stability. Our study illustrates the crucial role of RNA quality control in RNA interference and reveals the elaborate mechanism that safeguards plant centromeres through epigenomic regulation.
 
Overall design Enzymatic Methyl-seq samples using 6-week-old leaves in WT, ccr4a ccr4b, ddm1rdr2, ddm1 rdr2 ccr4a ccr4b.
 
Contributor(s) Shimada A, Saze H
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Submission date Aug 07, 2024
Last update date Aug 26, 2024
Contact name ATSUSHI SHIMADA
Organization name Okinawa Institute of Science and Technology
Department Plant Epigenetics Unit
Lab Saze Lab
Street address 1919-1 Tancha
City Onna-son, Kunigami-gun, Okinawa
ZIP/Postal code 904-0495
Country Japan
 
Platforms (1)
GPL26208 Illumina NovaSeq 6000 (Arabidopsis thaliana)
Samples (4)
GSM8444941 EM-seq, WT, adult leaves
GSM8444942 EM-seq, ccr4a ccr4b, adult leaves
GSM8444943 EM-seq, ddm1 rdr2, adult leaves
Relations
BioProject PRJNA1145382

Download family Format
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE274196_RAW.tar 857.0 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA

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